Biology subjects

Hildt, E.

Publications and source records attributed to Hildt, E..

6 recordsLinked to original sources

bioRxiv2026

Reversal effects of Isochlorogenic acid A on HBV-induced transcriptional dysregulation and apoptotic signaling

Chronic hepatitis B virus (HBV) infection contributes to hepatocellular carcinoma by disrupting host transcription, cell-cycle control, and apoptotic signaling. Isochlorogenic acid A (ICAA), a natural compound with antiviral and hepatoprotective properties, was previously shown to inhibit HBV replication by interfering with multiple steps of the viral life cycle. Because chronic HBV often reflects an imbalance between proliferation and cell death, we investigated how ICAA affects gene expression related to these processes in the presence or absence of HBV. We performed transcriptome analysis using RNA sequencing (RNA-seq) in HepAD38 cells (a HepG2-derived stable HBV-expressing line) and HepG2 control cells (HBV-negative) treated with ICAA or DMSO. HBV caused major differences in gene expression in HepAD38 cells compared with HBV-negative HepG2 cells. Principal component analysis showed that ICAA significantly altered HBV-dependent expression patterns, resulting in 189 differentially expressed genes (DEGs) that were regulated in opposite directions by both HBV and ICAA. Functional enrichment analysis highlighted pathways in viral carcinogenesis, apoptosis, MAPK signaling, and p53 signaling. Annexin V/propidium iodide assays showed apoptotic cells in both treated and untreated HepAD38 cultures, with only minor pattern changes. Mechanistically, in untreated HBV-positive cells caspase-9 cleavage failed to activate PARP, suggesting that induction of intrinsic apoptosis is followed by blocked execution. In contrast, ICAA inhibits caspase-9 cleavage in a dose-dependent manner, while activating PARP. Consistent with this, ICAA treatment increased apoptotic DNA fragmentation in HepAD38, reflecting the proapoptotic potential of ICAA under these conditions facilitating the elimination of HBV-positive cells by apoptosis. These findings highlight the potential therapeutic relevance of this compound in processes associated with HBV pathogenesis, together with its antiviral effect. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/733975v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@38d107org.highwire.dtl.DTLVardef@235a13org.highwire.dtl.DTLVardef@ee988aorg.highwire.dtl.DTLVardef@60cb13_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

The intertwined fate: exploring the hepatitis C virus/Nrf1 crosstalk

BACKGROUNDDespite advances in knowledge and medicine, hepatitis C virus (HCV) infection remains a global challenge. The viral life cycle depends heavily on lipid metabolism; consequently, HCV infection is associated with significant alterations to host lipid homeostasis. One of the regulators maintaining this homeostasis is the transcription factor nuclear factor erythroid 2-related factor 1 (Nrf1). There are multiple Nrf1 proteoforms that differ in their capacity to act as a cholesterol sensor or to activate or inhibit gene expression. Previously, we identified that the amount of full-length Nrf1 protein in HCV-replicating cells is significantly reduced. In this study, we investigate whether HCV affects the formation and functionality of the different Nrf1 proteoforms, and whether this contributes to the HCV-dependent dysregulation of cellular lipid metabolism. METHODSThe HCV-Nrf1 crosstalk was characterized using robust methods including: Western blot, FRET Acceptor Photobleaching assay, reverse transcriptase-polymerase chain reaction and confocal laser scanning microscopy-based approaches. RESULTSHCV infection does not alter the onset of Nrf1 proteoforms generated through proteasomal cleavage of the protein. However, the amount of different Nrf1 proteoforms is significantly reduced in HCV-positive cells due to enhanced Nrf1 turnover. Furthermore, the Nrf1 proteoforms with transcriptional activator functions are prevented from translocation into the nucleus. Reduced Nrf1 activity contributes to elevated cholesterol levels and favors lipid droplets formation. Conversely, rescue of Nrf1 activity in HCV-replicating cells is associated with decreased intracellular cholesterol levels, reduced number of lipid droplets and impaired viral release reflected by intracellular accumulation of the core protein and intact viral particles. CONCLUSIONSOverall, our results identify Nrf1 as a significant factor in the deregulation of host lipid metabolism induced by HCV. The inhibition of Nrf1 functionality driven by HCV leads to intracellular cholesterol accumulation, resulting in enhanced lipid droplet formation that supports the HCV life cycle and contributes to HCV-associated pathogenesis.

microbiology↗

bioRxiv2026

pyKinaXe: a fast and robust turnkey kinase activity profiler with high resolution

MotivationPeptide microarray technologies such as PamGenes enable direct measurement of peptide phosphorylation by upstream kinases, yet extraction of kinases from raw data depends on proprietary software or separate open-source alternatives delivering time-consuming processing across a variety of different steps, limiting throughput for experimental large-scale kinome generation in clinical and research settings. ResultsWe developed pyKinaXe, a Python package for automated end-to-end analysis of PamChip(R) data, integrating robust image processing, quantification of phosphorylation kinetics, multi-database substrate-kinase mapping, and upstream kinase analysis into a single one-click pipeline. Validation on a selected published benchmark dataset recovered 76-89% of the signaling pathways for previously reported significantly deregulated kinases. Processing time was reduced on the same data from over 30 minutes to[~] 25 seconds, leading to a 75-fold speed increase compared to other open-source alternatives. Thus, pyKinaXe addresses the key limitations of existing peptide-microarray-based kinase activity inference tools (slow inference, fragmented workflows, and poor usability) enabling fast and robust analysis, and facilitating high-throughput experiments and large-scale kinome profiling. Availability and implementationpyKinaXe is implemented in Python 3.13 and distributed under the Apache 2.0 License. Source code, documentation, and installation instructions are freely available at https://github.com/pykinaxe/pyKinaXe. The benchmark data is available at Mendeley Data (doi: 10.17632/ynp7f92n47.1). A pyKinaXes user-friendly web-based interface can be accessed at https://pykinaxe.github.io/home.

bioinformatics↗

bioRxiv2024

Late stages of the Zika virus life cycle are impaired by a selective TRPML2 agonist

The flavivirus genus includes human pathogenic viruses such as Dengue (DENV), West Nile (WNV) and Zika virus (ZIKV) posing a global health threat due to limited treatment options. Ion channels are crucial for various viral life cycle stages, but their potential as targets for antivirals is often not fully realized due to the lack of selective modulators. Here, we observe that the human endolysosomal cation channel TRPML2 agonist ML2-SA1 impairs the late life cycle stages of ZIKV, thus underscoring TRPML2 as a promising antiviral target. Upon treatment with ML2-SA1, levels of intracellular genomes and number of released virus particles of two different ZIKV isolates were significantly reduced. ML2-SA1-treated cells displayed enlarged vesicular structures and multivesicular bodies with ZIKV envelope protein accumulation. However, no increased ZIKV degradation in lysosomal compartments was observed. Rather, the antiviral effect of ML2-SA1 seemed to manifest by the compounds negative impact on genome replication. Moreover, ML2-SA1 treatment also led to intracellular cholesterol accumulation. ZIKV as well as many other viruses including the Orthohepevirus Hepatitis E virus (HEV) rely on the endolysosomal system and are affected by intracellular cholesterol levels to complete their life cycle. Since we observed ML2-SA1 to also negatively impact HEV infections in vitro, this compound may harbor a broader antiviral potential through perturbing the intracellular cholesterol distribution. Besides underscoring the potential of TRPML2 as a promising target for combatting viral infections, we uncover a tentative connection between this protein and cholesterol distribution within the context of infectious diseases.

cell biology↗

bioRxiv2021

Acute myeloid leukemia cells are targeted by the naturally occurring CXCR4 antagonist EPI-X4

This manuscript has been withdrawn by the authors as no consent could be achieved with regard to data contribution. Based on this no agreement on authorship and/or listing in the acknowledgement section was reached. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

cancer biology↗

bioRxiv2020

CXCR4 signaling is counteracted by the naturally occurring CXCR4 antagonist EPI-X 4 in Waldenstrom Macroglobulinemia

CXCR4 expression and downstream signaling have been identified as key factors in malignant hematopoiesis. Thus, up to 40% of all patients with Waldenstroms Macroglobulinemia (WM) carry an activating mutation of CXCR4 that leads to a more aggressive clinical course and inferior outcome upon treatment with the Brutons tyrosine kinase inhibitor ibrutinib. Nevertheless, little is known about physiological mechanisms counteracting CXCR4 signaling in hematopoietic neoplasms. Recently, the endogenous human peptide EPI-X4 was identified as a natural CXCR4 antagonist that effectively blocks CXCL12-mediated receptor internalization and suppresses the migration and invasion of cancer cells towards a CXCL12 gradient. Here, we demonstrate that EPI-X4 efficiently impairs growth of WM cells in vitro and in vivo and blocks their migration towards CXCL12. The CXCR4 inhibitory activity of EPI-X4 is accompanied by decreased expression of genes involved in MAPK signaling and energy metabolism. Notably, the anti-WM activity of EPI-X4 could be further augmented by the rational design of EPI-X4 derivatives showing higher binding affinity to CXCR4. In summary, these data demonstrate that a naturally occurring anti-CXCR4 peptide is able to interfere with WM growth, and that optimized derivatives of EPI-X4 may represent a promising approach in suppressing growth promoting CXCR4 signaling in WM.

cancer biology↗